Fleet admiral > admiral.
Akainu's fight with aokiji made him stronger. Clearly.
So fleet admrial akainu > admiral akainu.
Yonko shanks > admiral akainu.
Yonko shanks = fleet admiral akainu (meaning they are very close powerwise, their fight would take probably 10 days or so and only then the winner would be decided)
That's the reason.
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Add to that fact akainu's injuries and his exhaustion because of his figth with whitebeard, shanks had clearly the upper hand.